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Remove max_ params for all other profiles
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@jfy133
jfy133 committed Oct 23, 2024
1 parent b5e346e commit 57762a7
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Showing 11 changed files with 200 additions and 126 deletions.
17 changes: 10 additions & 7 deletions conf/test_bakta.config
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Expand Up @@ -10,14 +10,17 @@
----------------------------------------------------------------------------------------
*/

params {
config_profile_name = 'AMP/ARG Bakta test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'
process {
resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '1.h'
]
}

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'
params {
config_profile_name = 'AMP/ARG Bakta test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'
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18 changes: 13 additions & 5 deletions conf/test_bgc_bakta.config
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Expand Up @@ -10,14 +10,22 @@
----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '1.h'
]
}

params {
config_profile_name = 'BGC Bakta test profile'
config_profile_description = 'Minimal test dataset to check BGC workflow function'
config_profile_name = 'BGC Bakta test profile'
config_profile_description = 'Minimal test dataset to check BGC workflow function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'
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28 changes: 18 additions & 10 deletions conf/test_bgc_prokka.config
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Expand Up @@ -10,24 +10,32 @@
----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '1.h'
]
}

params {
config_profile_name = 'BGC Prokka test profile'
config_profile_description = 'Minimal test dataset to check BGC workflow function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'

annotation_tool = 'prokka'
annotation_tool = 'prokka'

run_arg_screening = false
run_amp_screening = false
run_bgc_screening = true
run_arg_screening = false
run_amp_screening = false
run_bgc_screening = true

bgc_run_hmmsearch = true
bgc_hmmsearch_models = 'https://raw.githubusercontent.com/antismash/antismash/fd61de057e082fbf071732ac64b8b2e8883de32f/antismash/detection/hmm_detection/data/ToyB.hmm'
bgc_run_hmmsearch = true
bgc_hmmsearch_models = 'https://raw.githubusercontent.com/antismash/antismash/fd61de057e082fbf071732ac64b8b2e8883de32f/antismash/detection/hmm_detection/data/ToyB.hmm'
}
28 changes: 18 additions & 10 deletions conf/test_bgc_pyrodigal.config
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Expand Up @@ -10,24 +10,32 @@
----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '1.h'
]
}

params {
config_profile_name = 'BGC Pyrodigal test profile'
config_profile_description = 'Minimal test dataset to check BGC workflow function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'

annotation_tool = 'pyrodigal'
annotation_tool = 'pyrodigal'

run_arg_screening = false
run_amp_screening = false
run_bgc_screening = true
run_arg_screening = false
run_amp_screening = false
run_bgc_screening = true

bgc_run_hmmsearch = true
bgc_hmmsearch_models = 'https://raw.githubusercontent.com/antismash/antismash/fd61de057e082fbf071732ac64b8b2e8883de32f/antismash/detection/hmm_detection/data/ToyB.hmm'
bgc_run_hmmsearch = true
bgc_hmmsearch_models = 'https://raw.githubusercontent.com/antismash/antismash/fd61de057e082fbf071732ac64b8b2e8883de32f/antismash/detection/hmm_detection/data/ToyB.hmm'
}
70 changes: 39 additions & 31 deletions conf/test_nothing.config
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Expand Up @@ -12,42 +12,50 @@
----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '1.h'
]
}

params {
config_profile_name = 'Test nothing profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'
amp_hmmsearch_models = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
bgc_hmmsearch_models = 'https://raw.githubusercontent.com/antismash/antismash/fd61de057e082fbf071732ac64b8b2e8883de32f/antismash/detection/hmm_detection/data/ToyB.hmm'

annotation_tool = 'pyrodigal'

run_arg_screening = false
run_amp_screening = false
run_bgc_screening = false

arg_fargene_hmmmodel = 'class_a,class_b_1_2'

amp_skip_amplify = true
amp_skip_macrel = true
amp_skip_ampir = true
amp_run_hmmsearch = false

arg_skip_deeparg = true
arg_skip_fargene = true
arg_skip_rgi = true
arg_skip_amrfinderplus = true
arg_skip_deeparg = true
arg_skip_abricate = true

bgc_skip_antismash = true
bgc_skip_deepbgc = true
bgc_skip_gecco = true
bgc_run_hmmsearch = false
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'
amp_hmmsearch_models = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
bgc_hmmsearch_models = 'https://raw.githubusercontent.com/antismash/antismash/fd61de057e082fbf071732ac64b8b2e8883de32f/antismash/detection/hmm_detection/data/ToyB.hmm'

annotation_tool = 'pyrodigal'

run_arg_screening = false
run_amp_screening = false
run_bgc_screening = false

arg_fargene_hmmmodel = 'class_a,class_b_1_2'

amp_skip_amplify = true
amp_skip_macrel = true
amp_skip_ampir = true
amp_run_hmmsearch = false

arg_skip_deeparg = true
arg_skip_fargene = true
arg_skip_rgi = true
arg_skip_amrfinderplus = true
arg_skip_deeparg = true
arg_skip_abricate = true

bgc_skip_antismash = true
bgc_skip_deepbgc = true
bgc_skip_gecco = true
bgc_run_hmmsearch = false
}
28 changes: 18 additions & 10 deletions conf/test_preannotated.config
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Expand Up @@ -10,24 +10,32 @@
----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '1.h'
]
}

params {
config_profile_name = 'ARG/AMP test profile - preannotated input'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_preannotated.csv'
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_preannotated.csv'

annotation_tool = 'pyrodigal'
annotation_tool = 'pyrodigal'

run_arg_screening = true
arg_fargene_hmmmodel = 'class_a,class_b_1_2'
run_arg_screening = true
arg_fargene_hmmmodel = 'class_a,class_b_1_2'

run_amp_screening = true
amp_run_hmmsearch = true
amp_hmmsearch_models = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
run_amp_screening = true
amp_run_hmmsearch = true
amp_hmmsearch_models = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
}
28 changes: 18 additions & 10 deletions conf/test_preannotated_bgc.config
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Original file line number Diff line number Diff line change
Expand Up @@ -10,24 +10,32 @@
----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '1.h'
]
}

params {
config_profile_name = 'BGC test profile - preannotated input'
config_profile_description = 'Minimal test dataset to check BGC workflow function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_preannotated.csv'
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_preannotated.csv'

annotation_tool = 'pyrodigal'
annotation_tool = 'pyrodigal'

run_arg_screening = false
run_amp_screening = false
run_bgc_screening = true
run_arg_screening = false
run_amp_screening = false
run_bgc_screening = true

bgc_run_hmmsearch = true
bgc_hmmsearch_models = 'https://raw.githubusercontent.com/antismash/antismash/fd61de057e082fbf071732ac64b8b2e8883de32f/antismash/detection/hmm_detection/data/ToyB.hmm'
bgc_run_hmmsearch = true
bgc_hmmsearch_models = 'https://raw.githubusercontent.com/antismash/antismash/fd61de057e082fbf071732ac64b8b2e8883de32f/antismash/detection/hmm_detection/data/ToyB.hmm'
}
28 changes: 18 additions & 10 deletions conf/test_prokka.config
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Original file line number Diff line number Diff line change
Expand Up @@ -10,24 +10,32 @@
----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '1.h'
]
}

params {
config_profile_name = 'AMP/ARG Prokka test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'

annotation_tool = 'prokka'
annotation_tool = 'prokka'

run_arg_screening = true
arg_fargene_hmmmodel = 'class_a,class_b_1_2'
run_arg_screening = true
arg_fargene_hmmmodel = 'class_a,class_b_1_2'

run_amp_screening = true
amp_run_hmmsearch = true
amp_hmmsearch_models = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
run_amp_screening = true
amp_run_hmmsearch = true
amp_hmmsearch_models = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
}
27 changes: 16 additions & 11 deletions conf/test_taxonomy_bakta.config
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Expand Up @@ -10,14 +10,25 @@
----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '1.h'
]
withName: MMSEQS_DATABASES {
memory = '14.GB'
}
}

params {
config_profile_name = 'Taxonomic classification test profile'
config_profile_description = 'Minimal test dataset to check taxonomic classification workflow function'
config_profile_name = 'Taxonomic classification test profile'
config_profile_description = 'Minimal test dataset to check taxonomic classification workflow function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '14.GB'
max_time = '6.h'
max_cpus = 2
max_memory = '14.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'
Expand All @@ -42,9 +53,3 @@ params {
bgc_antismash_contigminlength = 1000
bgc_run_hmmsearch = true
}

process {
withName: MMSEQS_DATABASES {
memory = '14.GB'
}
}
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